scholarly journals HYpro16: A Two-Proteome Mixture to Assess Interference in Isobaric Tag-Based Sample Multiplexing Experiments

2020 ◽  
Vol 32 (1) ◽  
pp. 247-254
Author(s):  
Jose Navarrete-Perea ◽  
Steven P. Gygi ◽  
Joao A. Paulo
Keyword(s):  
Isobaric Tag

Assessing interference in isobaric tag‐based sample multiplexing using an 18‐plex interference standard

PROTEOMICS ◽  
2021 ◽  
pp. 2100317
Author(s):  
Jose Navarrete‐Perea ◽  
Xinyue Liu ◽  
Ramin Rad ◽  
Jeremy P. Gygi ◽  
Steven P. Gygi ◽  
...  
Keyword(s):  
Isobaric Tag

scholarly journals A Versatile Isobaric Tag Enables Proteome Quantification in Data-Dependent and Data-Independent Acquisition Modes

2020 ◽  
Vol 92 (24) ◽  
pp. 16149-16157
Author(s):  
Xiaobo Tian ◽  
Marcel P. de Vries ◽  
Hjalmar P. Permentier ◽  
Rainer Bischoff
Keyword(s):  
Data Independent Acquisition ◽  
Isobaric Tag

scholarly journals Proteomic Analysis of Beef Tenderloin and Flank Assessed Using an Isobaric Tag for Relative and Absolute Quantitation (iTRAQ)

Animals ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 150
Author(s):  
Zhaomin Lei ◽  
Jianping Wu ◽  
Deyin Zhang ◽  
Ting Liu ◽  
Shengguo Zhao ◽  
...  
Keyword(s):  
Proteomic Analysis ◽  
Expression Patterns ◽  
Tca Cycle ◽  
Absolute Quantification ◽  
Absolute Quantitation ◽  
Oxidation Reduction ◽  
The Tca Cycle ◽  
Isobaric Tag ◽  
Isobaric Tags

Herein, we performed a proteomic analysis of tenderloin and flank steaks from Simmental cattle using the isobaric tags for a relative and absolute quantification (iTRAQ) approach. We identified 17 amino acids in both steaks, and Gly, Cys, Ile, Lys, and Pro differed most in abundance between the steak types (p < 0.05). A comparison of the expression patterns in steaks revealed 128 differentially expressed proteins (DEPs), of which 44 were up-regulated and 84 were down-regulated. Furthermore, 27 DEPs (p < 0.05) were subjected to gene ontology (GO) analysis, and many were found to be related to oxidation-reduction, metabolism, hydrogen ion transmembrane transport, transport, the tricarboxylic acid (TCA) cycle, mitochondrial electron transport, and the conversion of nicotinamide adenine dinucleotide (NADH) to ubiquinone. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis also implicated these DEPs in various signalling pathways, including oxidative phosphorylation, cardiac muscle contraction, the TCA cycle, biosynthesis, and the metabolism. These findings provide a new insight into key proteins involved in the determination of amino acid composition in beef.

scholarly journals Trends in the Design of New Isobaric Labeling Reagents for Quantitative Proteomics

Molecules ◽  
2019 ◽  
Vol 24 (4) ◽  
pp. 701 ◽  
Author(s):  
Remigiusz Bąchor ◽  
Mateusz Waliczek ◽  
Piotr Stefanowicz ◽  
Zbigniew Szewczuk
Keyword(s):  
Mass Spectrometry ◽  
Quantitative Proteomics ◽  
Chemical Properties ◽  
High Energy ◽  
Tandem Mass ◽  
Peptide Molecule ◽  
Wide Range ◽  
Potential Applications ◽  
Isobaric Tag ◽  
Modern Mass

Modern mass spectrometry is one of the most frequently used methods of quantitative proteomics, enabling determination of the amount of peptides in a sample. Although mass spectrometry is not inherently a quantitative method due to differences in the ionization efficiency of various analytes, the application of isotope-coded labeling allows relative quantification of proteins and proteins. Over the past decade, a new method for derivatization of tryptic peptides using isobaric labels has been proposed. The labels consist of reporter and balanced groups. They have the same molecular weights and chemical properties, but differ in the distribution of stable heavy isotopes. These tags are designed in such a way that during high energy collision induced dissociation (CID) by tandem mass spectrometry, the isobaric tag is fragmented in the specific linker region, yielding reporter ions with different masses. The mass shifts among the reporter groups are compensated by the balancing groups so that the overall mass is the same for all forms of the reagent. Samples of peptides are labeled with the isobaric mass tags in parallel and combined for analysis. Quantification of individual peptides is achieved by comparing the intensity of reporter ions in the tandem mass (MS/MS) spectra. Isobaric markers have found a wide range of potential applications in proteomics. However, the currently available isobaric labeling reagents have some drawbacks, such as high cost of production, insufficient selectivity of the derivatization, and relatively limited enhancement of sensitivity of the analysis. Therefore, efforts have been devoted to the development of new isobaric markers with increased usability. The search for new isobaric markers is focused on developing a more selective method of introducing a tag into a peptide molecule, increasing the multiplexicity of markers, lowering the cost of synthesis, and increasing the sensitivity of measurement by using ionization tags containing quaternary ammonium salts. Here, the trends in the design of new isobaric labeling reagents for quantitative proteomics isobaric derivatization strategies in proteomics are reviewed, with a particular emphasis on isobaric ionization tags. The presented review focused on different types of isobaric reagents used in quantitative proteomics, their chemistry, and advantages offer by their application.

scholarly journals Identification of novel pathways in pathogenesis of ketosis in dairy cows via iTRAQ/MS

2016 ◽  
Vol 60 (3) ◽  
pp. 309-314 ◽  
Author(s):  
Shi Shu ◽  
Chuchu Xu ◽  
Cheng Xia ◽  
Xinhuan Xiao ◽  
Gang Wang ◽  
...  
Keyword(s):  
Protein Expression ◽  
Dairy Cows ◽  
Expression Profiles ◽  
The Novel ◽  
Absolute Quantitation ◽  
Subclinical Ketosis ◽  
Isobaric Tag ◽  
Production Increase ◽  
Protein Expression Profiles ◽  
New Evidence

AbstractIntroduction: To identify novel pathways involved in the pathogenesis of ketosis, an isobaric tag for relative and absolute quantitation/mass spectrometry was used to define differences in protein expression profiles between healthy dairy cows and those with clinical or subclinical ketosis.Material and Methods: To define the novel pathways of ketosis in cattle, the differences in protein expression were analysed by bioinformatics. Go Ontology and Pathway analysis were carried out for enrich the role and pathway of the different expression proteins between healthy dairy cows and those with clinical or subclinical ketosis.Results: Differences were identified in 19 proteins, 16 of which were relatively up-regulated while the remaining 3 were relatively down-regulated. Sorbitol dehydrogenase (SORD) and glyceraldehyde-3-phosphate dehydrogenase (G3PD) were up-regulated in cattle with ketosis. SORD and G3PD promoted glycolysis. These mechanisms lead to pyruvic acid production increase and ketone body accumulation.Conclusion: The novel pathways of glycolysis provided new evidence for the research of ketosis.

scholarly journals Investigation of the Protective Effects of Phlorizin on Diabetic Cardiomyopathy indb/dbMice by Quantitative Proteomics

2013 ◽  
Vol 2013 ◽  
pp. 1-9 ◽  
Author(s):  
Qian Cai ◽  
Baoying Li ◽  
Fei Yu ◽  
Weida Lu ◽  
Zhen Zhang ◽  
...  
Keyword(s):  
Diabetic Cardiomyopathy ◽  
Body Weight Gain ◽  
Fasting Blood Glucose ◽  
Interaction Network ◽  
Diabetic Patients ◽  
Protective Effects ◽  
Absolute Quantitation ◽  
Patients With Diabetes ◽  
Itraq Proteomics ◽  
Isobaric Tag

Patients with diabetes often develop hypertension and atherosclerosis leading to cardiovascular disease. However, some diabetic patients develop heart failure without hypertension and coronary artery disease, a process termed diabetic cardiomyopathy. Phlorizin has been reported to be effective as an antioxidant in treating diabetes mellitus, but little is known about its cardioprotective effects on diabetic cardiomyopathy. In this study, we investigated the role of phlorizin in preventing diabetic cardiomyopathy indb/dbmice. We found that phlorizin significantly decreased body weight gain and the levels of serum fasting blood glucose (FBG), triglycerides (TG), total cholesterol (TC), and advanced glycation end products (AGEs). Morphologic observations showed that normal myocardial structure was better preserved after phlorizin treatment. Using isobaric tag for relative and absolute quantitation (iTRAQ) proteomics, we identified differentially expressed proteins involved in cardiac lipid metabolism, mitochondrial function, and cardiomyopathy, suggesting that phlorizin may prevent the development of diabetic cardiomyopathy by regulating the expression of key proteins in these processes. We used ingenuity pathway analysis (IPA) to generate an interaction network to map the pathways containing these proteins. Our findings provide important information about the mechanism of diabetic cardiomyopathy and also suggest that phlorizin may be a novel therapeutic approach for the treatment of diabetic cardiomyopathy.

scholarly journals Identification of Novel Biomarker Candidates for Hypertrophic Cardiomyopathy and Other Cardiovascular Diseases Leading to Heart Failure

2016 ◽  
pp. 751-762 ◽  
Author(s):  
H. REHULKOVA ◽  
P. REHULKA ◽  
A. MYSLIVCOVA FUCIKOVA ◽  
J. STULIK ◽  
R. PUDIL
Keyword(s):  
Hypertrophic Cardiomyopathy ◽  
Cardiovascular Diseases ◽  
Stable Coronary Artery Disease ◽  
Specific Protein ◽  
Protein Markers ◽  
Protein Biomarkers ◽  
Absolute Quantitation ◽  
Obstructive Hypertrophic Cardiomyopathy ◽  
Isobaric Tag ◽  
Cardiovascular Pathologies

In-depth proteome discovery analysis represents new strategy in an effort to identify novel reliable specific protein markers for hypertrophic cardiomyopathy and other life threatening cardiovascular diseases. To systematically identify novel protein biomarkers of cardiovascular diseases with high mortality we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteome technology to make comparative analysis of plasma samples obtained from patients suffering from non-obstructive hypertrophic cardiomyopathy, stable dilated cardiomyopathy, aortic valve stenosis, chronic stable coronary artery disease and stable arterial hypertension. We found 128 plasma proteins whose abundances were uniquely regulated among the analyzed cardiovascular pathologies. 49 of them have not been described yet. Additionally, application of statistical exploratory analyses of the measured protein profiles indicated the relationship in pathophysiology of the examined cardiovascular pathologies.

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